Innovative regents have historically driven breakthroughs in biomedical science; we propose to develop proteomic reagents and technologies to power comprehensive biomarker and target discover for detection, prognosis, patient stratification, and therapeutics in cancer. The technical hurdles in proteomics are sample preparation (separation) and quantification. We propose to develop noel reagents for affinity mass tagging that enable separation and differential profiling of protein samples from three (or more) closely related but distinct physiological states, e.g. from normal, cancer, and drug-treated individuals. One of these uses DNA as a tunable affinity tag that can be exploited in multiplexed capture on nanoparticles with complementary DNA. These are integrated into a Flag tag-based Protein Separation (FLAPS) strategy that may achieve pre-fractionation of the proteome as well as differential profiling. The combination of amino acid-specific (Phase I) and class- specific (in a future Phase II proposal) capture coupled with nanoparticle arrays in solution will also be the basis for custom arrays specifically tailored to profiling of mitogenic pathways, apoptotic pathways, or specific post-translational modifications. These will be useful for both a biomarker discovery phase as well as for assessing therapeutic efficacy of drugs or their toxicity that is the goal of patient-tailored drug treatment. PROPOSED COMMERCIAL APPLICATIONS: The protein modification reagents to be developed under this grant will provide a solution to the rate-limiting steps in proteomics research: protein separation and quantification-a rapidly growing market estimated to be $1.5 B. The technologies will particularly facilitate direct comparison of proteins from different samples (cell lines, time points, treatments) and therefore shortening drug-discovery and development.